MolNFT v1 · #140836 · protein

Structure of house dust mite allergen der F 21 in PEG2KMME

5YNY: “Structure of house dust mite allergen der F 21 in PEG2KMME”. X-ray diffraction, 7 pockets (best druggability 0.73). MolNFT v1 #140836 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5YNY
Type: protein
Length: 454 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Allergen der F 21
UniProt: B2GM84
Pockets: 7 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 81% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Allergen der F 21	protein	115	80% helix, 0% strand	B2GM84
B	Allergen der F 21	protein	116	79% helix, 0% strand	B2GM84
C	Allergen der F 21	protein	112	82% helix, 0% strand	B2GM84
D	Allergen der F 21	protein	111	83% helix, 0% strand	B2GM84

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	184	0.73	0.89	33	empty
2	286	0.72	0.85	46	empty
3	396	0.62	0.77	38	empty
4	61	0.47	0.84	16	empty
5	63	0.36	0.78	16	empty

Interfaces

4 interfaces between chains.

A–B · 1328 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 1097 Å² buried · 17 hydrogen bonds · protein-protein
B–D · 98 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 27 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5YNY · Structure of house dust mite allergen Der F 21 in PEG2KMME · the same entry in another collection · chain D against D, TM-score 1.00
B2GM84 · AlphaFold monomer V2.0 prediction for mite allergen der F 21.0101 (B2GM84) · a predicted model of the same protein · chain C against A, TM-score 0.97

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt B2GM84
Elsewhere: RCSB PDB 5YNY · PDBe 5YNY · UniProt B2GM84

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